|
| Status |
Public on Feb 17, 2011 |
| Title |
squamous cell carcinoma, biological replicate 18 |
| Sample type |
RNA |
| |
|
| Source name |
cervix
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: squamous cell carcinoma
age of ffpe block (years): 11
p63 staining status: +
|
| Treatment protocol |
not applicable
|
| Growth protocol |
not applicable
|
| Extracted molecule |
total RNA |
| Extraction protocol |
3 x 20uM sections of FFPE material was used for all samples. Total RNA was recovered using the Recoverall (Ambion kit) as per manufactures instructions.
|
| Label |
biotin
|
| Label protocol |
The RNA was amplified using the WT-Ovation Pico RNA Amplification System, converted using the WT-Ovation Exon Module, and fragmented and labelled using the NuGEN FL-Ovation cDNA Biotin Module v2.
|
| |
|
| Hybridization protocol |
RNA was quantified using a Bioanalyser (Agilent Technologies) and 100 ng amplified using NuGEN WT-Ovation FFPE v2 kit. The WT-Ovation Exon Module V1.0 was used to generate ST-cDNA and 4 µg was hybridised to Affymetrix Human Exon 1.0 ST arrays.
|
| Scan protocol |
Affymetrix GeneChip 3000 running GCOS software.
|
| Description |
V590
0310_CaW(4)22_ExH_nuFFPE_V590.CEL
|
| Data processing |
Background adjustment, quantile normalisation and summarisation of probe-level intensity were performed with the Robust Multi-array Average (RMA) algorithm.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: not applicable
|
| |
|
| Submission date |
Feb 17, 2011 |
| Last update date |
Feb 17, 2011 |
| Contact name |
Hui Sun Leong |
| E-mail(s) |
HuiSun.Leong@cruk.manchester.ac.uk
|
| Organization name |
Cancer Research UK Manchester Institute
|
| Department |
The University of Manchester
|
| Lab |
Computational Biology Support Team
|
| Street address |
Wilmslow Road
|
| City |
Manchester |
| ZIP/Postal code |
M20 4BX |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL5188 |
| Series (1) |
| GSE27388 |
Exon-array profiling of squamous cell carcinoma and adenocarcinoma in human cervical FFPE samples |
|
